Thinking ahead: Bacteria anticipate coming changes in their environment

Jun 09, 2008

A new study by Princeton University researchers shows for the first time that bacteria don't just react to changes in their surroundings -- they anticipate and prepare for them. The findings, reported in the June 6 issue of Science, challenge the prevailing notion that only organisms with complex nervous systems have this ability.

"What we have found is the first evidence that bacteria can use sensed cues from their environment to infer future events," said Saeed Tavazoie, an associate professor of molecular biology, who conducted the study along with graduate student Ilias Tagkopoulos and postdoctoral researcher Yir-Chung Liu.

The research team, which included biologists and engineers, used lab experiments to demonstrate this phenomenon in common bacteria. They also turned to computer simulations to explain how a microbe species' internal network of genes and proteins could evolve over time to produce such complex behavior.

"The two lines of investigation came together nicely to show how simple biochemical networks can perform sophisticated computational tasks," said Tavazoie.

In addition to shedding light on deep questions in biology, the findings could have many practical implications. They could help scientists understand how bacteria mutate to develop resistance to antibiotics. They also may help in developing specialized bacteria to perform useful tasks such as cleaning up environmental contamination.

In one part of the study, the researchers studied the behavior of E. coli, the ubiquitous bacterium that travels back and forth between the environment and the gut of warm-blooded vertebrates. They wanted to explain a long-standing question about the bug: How do its genes respond to the temperature and oxygen changes that occur when the bacterium enters the gut?

The conventional answer is that it reacts to the change -- after sensing it -- by switching from aerobic (oxygen) to anaerobic (oxygen-less) respiration. If this were true, however, the organism would be at a disadvantage during the time it needed to make the switch. "This kind of reflexive response would not be optimal," Tavazoie said.

The researchers proposed a better strategy for the bug. During E. coli's life cycle, oxygen level is not the only thing that changes -- it also experiences a sharp rise in temperature when it enters an animal's mouth. Could this sudden warmth cue the bacterium to prepare itself for the subsequent lack of oxygen?

To test this idea, the researchers exposed a population of E. coli to different temperatures and oxygen changes, and measured the gene responses in each case. The results were striking: An increase in temperature had nearly the same effect on the bacterium's genes as a decrease in oxygen level. Indeed, upon transition to a higher temperature, many of the genes essential for aerobic respiration were practically turned off.

To prove that this is not just genetic coincidence, the researchers then grew the bacteria in a biologically flipped environment where oxygen levels rose following an increase in temperature. Remarkably, within a few hundred generations the bugs partially adapted to this new regime, and no longer turned off the genes for aerobic respiration when the temperature rose.

"This reprogramming clearly indicates that shutting down aerobic respiration following a temperature increase is not essential to E. coli's survival," said Tavazoie. "On the contrary, it appears that the bacterium has "learned" this response by associating specific temperatures with specific oxygen levels over the course of its evolution."

Lacking a brain or even a primitive nervous system, how is a single-celled bacterium able to pull off this feat? While higher animals can learn new behavior within a single lifetime, bacterial learning takes place over many generations and on an evolutionary time scale, Tavazoie explained. To gain a deeper understanding of this phenomenon, his team developed a virtual microbial ecosystem, called "Evolution in Variable Environment." Each microbe in this novel computational framework is represented as a network of interacting genes and proteins. An evolving population of these virtual bugs competes for limited resources within a changing environment, mimicking the behavior of bacteria in the real world.

To implement this framework, the researchers had to deal with the sheer scale and complexity of simulating any realistic biological system. They had to keep track of hundreds of genes, proteins and other biological factors in the microbial population, and observe them as they varied over millions of time points. "Simulations at this scale and complexity would have been impossible in the past," said Tagkopoulos. Even with the vast number crunching power the supercomputers provided by the University's computational science and engineering support group, their experiments took nearly 18 months to run, said Tagkopoulos.

In this virtual world, microbes are more likely to survive if they conserve energy by mostly turning off the biological processes that allow them to eat. The challenge they face then is to anticipate the arrival of food and turn up their metabolism just in time. To help them along, the researchers gave the bugs cues before feeding them, but the cues had to appear in just the right pattern to indicate that food was on its way.

"To predict mealtimes accurately, the microbes would have to solve logic problems," said Tagkopoulos, a fifth-year graduate student in electrical engineering and the principal architect of the Evolution in Variable Environment framework.

And sure enough, after a few thousand generations, an ecologically fit strain of microbe emerged which did exactly that. This happened for every pattern of cues that the researchers tried. The feeding response of these gastronomically savvy bugs peaked just when food was offered, said Tagkopoulos.

When the researchers examined a number of fit virtual bugs, they could at first make little sense out of them. "Their biochemical networks were filled with seemingly unnecessary components," said Tagkopoulos. "That is not how an engineer would design logic-solving networks." Pared down to their essential elements, however, the networks revealed a simple and elegant structure. The researchers could now trace the different sequences of gene and protein interactions organisms used in order to respond to cues and anticipate mealtimes. "It gave us insights into how simple organisms such as bacteria can process information from the environment to anticipate future events," said Tagkopoulos.

The researchers said that their findings open up many exciting avenues of research. They are planning to use similar methods to study how bacteria exchange genes with one another (horizontal gene transfer), how tissues and organs develop (morphogenesis), how viral infections spread and other core problems in biology.

"What is really exciting about our discovery is that it brings together and establishes deep connections between the traditionally separate fields of microbial ecology, network evolution and behavior," said Tavazoie.

Source: Princeton University

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HenisDov
not rated yet Jun 09, 2008
Comment at:

http://www.physfo...ic=14988&st=225&#entry347802

Dov Henis
HenisDov
not rated yet Jun 09, 2008

http://www.physfo...ic=14988&st=225&#entry347802
HenisDov
not rated yet Jun 10, 2008
News are catching up with us...

"Bacteria Anticipate Coming Changes In Their Environment"


2008
http://www.prince...pstories

2003
http://www.pubmed...=1315802


Our long-ago titles:

http://www.physfo...ic=14988]http://www.physfo...ic=14988[/url]&st=225&#entry347802

Culture Is Biology, It Imprints Genetics, Drives Evolution.

Darwinism Corrected To Tomorrow's Comprehension.

Darwinians, It Is Culture That Drives Evolution Since Life's Day One!


Culture is a basic biological entity. It is a ubiquitous elaboration/extension of genome's activity beyond its outermost cell membrane and of multicelled organisms' behaviour. It has been selected for survival of the genome as means of extending its exploitation capabilities of the out-of-cell circumstances, consequent to the earlier evolution and selection of the genome's organ, its outermost cell membrane, for controlling the inside-of-cell genes'-commune environmental circumstances.


March 16 2008
http://www.physfo...ic=14988]http://www.physfo...ic=14988[/url]&st=165&#entry323376

"By plain common sense it is therefore culture, the ubiqitous biological entity, that drives earth life evolution."

March 1 2008
"Culture Is Biology, It Imprints Genetics"

http://forum.phys...ic=14988&st=165&#entry316631



I. Quotes from "Chimp and human communication trace to same brain region"

http://www.eureka...2108.php

" An area of the brain involved in the planning and production of spoken and signed language in humans plays a similar role in chimpanzee communication.

This might be interpreted in one of two ways:

One interpretation of our results is that chimpanzees have, in essence, a %u2018language-ready brain'. By this, we are suggesting that apes are born with and use the brain areas identified here when producing signals that are part of their communicative repertoire.

Alternatively, one might argue that, because our apes were captive-born and producing communicative signals not seen often in the wild, the specific learning and use of these signals %u2018induced%u2019 the pattern of brain activation we saw. This would suggest that there is tremendous plasticity in the chimpanzee brain, as there is in the human brain, and that the development of certain kinds of communicative signals might directly influence the structure and function of the brain."


II. Quotes from earlier postings in this thread:

Culture Is Biology, It Affects Genetics

The Common Mistake: Genetic Changes Have NOT Made Us Human; Human Culture Has Been Changing Our Genetics.

A. http://www.eureka...0607.php

Are humans evolving faster?
Findings suggest we are becoming more different, not alike.

B. http://www.eureka...0507.php

Genome study places modern humans in the evolutionary fast lane.

C. http://blog.360.y...Q--?cq=1]http://blog.360.y...Q--?cq=1[/url]]http://blog.360.y...Q--?cq=1[/url]&p=207

From my postings way back in 2005, which cites genetic evidence/demonstration of the workings of human cultural evolution:

- From Science, 2 Sept 2005: "Page's team compared human and chimp Ys to see whether either lineage has lost functional genes since they split.

The researchers found that the chimp had indeed suffered the slings and arrows of evolutionary fortune. Of the 16 functional genes in this part of the human Y, chimps had lost the function of five due to mutations. In contrast, humans had all 11 functional genes also seen on the chimp Y. "The human Y chromosome hasn't lost a gene in 6 million years," says Page. "It seems like the demise of the hypothesis of the demise of the Y," says geneticist Andrew Clark of Cornell University in Ithaca, New York.

Chimp's genome has been continuing survival by physiologically adapting to changing environments.

- But look at this: From Science, Vol 309, 16 Sept 2005, Evolving Sequence and Expression:"An analysis of the evolution of both gene sequences and expression patterns in humans and chimpanzees...shows that...surprisingly, genes expressed in the brain have changed more on the human lineage than on the chimpanzee lineage, not only in terms of gene expression but also in terms of amino acid sequences".

Surprisingly...???

Human's genome continued survival mainly by modifying-controling its environment.

- And I suggest that detailed study of other creatures that, like humans, underwent radical change of living circumstances, for example ocean-dwelling mammals, might bring to light unique effects of culture-evolution processes and features of evolutionary implications parallel to those of humans.


D. Chapter II, Life, Tomorrow's Comprehension:

http://blog.360.y...Q--?cq=1]http://blog.360.y...Q--?cq=1[/url]]http://blog.360.y...Q--?cq=1[/url]&p=372

Natural Selection Is A Two Level Interdependent Affair

1) Evolution ensues from genome/genes modifications ("mutations"), inherently ever more of them as new functional options arise for the organism.

2) Modifications of genome's functional capabilities can be explained by the second-stratum organism's culture-life-experience feedbacks to its genome, its prime/base organism. The route-modification selection of a replicating gene, when it is at its alternative-splicing-steps junctions, is biased by the feedback gained by the genome, the parent organism, from the culture-life-experience of its progeny big organism. THIS IS HOW EVOLUTION COMES ABOUT.

3) The challenge now is to figure out the detailed seperate steps involved in introducing and impressing the big organism's experiences (culture) feedbacks on its founding parents' genome's genes, followed by the detailed seperate steps involved in biasing-directing the genes to prefer-select the biased-favored splicing.

4) I find it astonishing that only very few persons, non-professional as well as professional biologists-evolutionists, have the clear conception that selection for survival occurs on two interdependent levels - (a) during the life of the second-stratum progeny organism in its environment, and (b) during the life of its genome, which is also an organism. Most, if not all, persons think - incorrectly - that evolution is about randomly occurring genes-genome modifications ("mutations") followed with selection by survival of the progeny organism in its environment. Whereas actually evolution is the interdependent , interactive and interenhencing selection at both the two above levels.


E. Eventually

Eventually it will be comprehended that things don't just "happen", "mutate", randomly in the base-prime organism, genome, constitution; the capability of the base-prime organisms to "happen" and "mutate" is indeed innate, but things "happen" and "mutate" not randomly but in biased directions, affected by the culture-experience feedback of the second level multi-cell organisms or of the mono-cell communities.


Dov Henis

http://blog.360.y...Q--?cq=1]http://blog.360.y...Q--?cq=1[/url]]http://blog.360.y...Q--?cq=1[/url]

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